Can one analyze advanced intercross lines (AIL)?
R/qtl has no special facilities for dealing with advanced intercross lines. One might analyze such data as if they were from an intercross, though with an expanded genetic map, but it is important to take account of the relationships among individuals (for example, the sibships in the final generation), and R/qtl is not currently able to do that. • Can one do a genome scan with a dominant, recessive, or additive allele model? No. In the analysis of intercross data, we always consider the full model (allowing the three genotypes to have different phenotype averages). One may inspect the results of effectplot to assess whether a locus appears to be dominant or additive. • Can one test if an allele is associated with an increase in phenotype? No, though one may inspect the results of effectplot which may suggest such an effect. We see little value in a formal significance test. • How can I estimate the heritability due to a QTL? One may use fitqtl to fit a multiple-QTL model and estimate
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